View source for Rn6 20-way conservation lastz parameters

==See Also==

<UL>
<LI>Rat 20-way [[Rn6 20-way Genome size statistics]]</LI>
<LI>Rat 20-way [[Rn6 20-way conservation alignment]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>


<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD></TR>

<TR><TD>
<TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
<TR><TH>G</TH><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>
<TR><TH>T</TH><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>90</TD><TD>-330</TD><TD>-236</TD><TD>-356</TD></TR>
<TR><TH>C</TH><TD>-330</TD><TD>100</TD><TD>-318</TD><TD>-236</TD></TR>
<TR><TH>G</TH><TD>-236</TD><TD>-318</TD><TD>100</TD><TD>-330</TD></TR>
<TR><TH>T</TH><TD>-356</TD><TD>-236</TD><TD>-330</TD><TD>90</TD></TR>
</TABLE>
O=600 E=150
</TD>
</TR></TABLE>

==do not edit, automatically generated table==
<TABLE BORDER=1>
<TR><TH>query</TH>
  <TH>abridged<BR>repeats(no)</TH>
  <TH>M(0)</TH><TH>K(3000)</TH>
  <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
  <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>
  <TH>O(400)</TH><TH>T(1)</TH>
  <TH>chain&nbsp;table<BR>date</TH>
  <TH>%&nbsp;of&nbsp;rn6<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkRn6)</TH>
</TR>
<TR>
  <TH>Mouse&nbsp;mm10</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2016-04-08</TD><TD ALIGN=RIGHT>71.015%</TD>
  <TD ALIGN=RIGHT>70.886%</TD></TR>
<TR>
  <TH>Prairie vole&nbsp;micOch1</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-18</TD><TD ALIGN=RIGHT>57.205%</TD>
  <TD ALIGN=RIGHT>70.134%</TD></TR>
<TR>
  <TH>Guinea pig&nbsp;cavPor3</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-13</TD><TD ALIGN=RIGHT>27.834%</TD>
  <TD ALIGN=RIGHT>28.362%</TD></TR>
<TR>
  <TH>Human&nbsp;hg38</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-17</TD><TD ALIGN=RIGHT>34.899%</TD>
  <TD ALIGN=RIGHT>31.077%</TD></TR>
<TR>
  <TH>Chimp&nbsp;panTro5</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-13</TD><TD ALIGN=RIGHT>40.816%</TD>
  <TD ALIGN=RIGHT>35.356%</TD></TR>
<TR>
  <TH>Tarsier&nbsp;tarSyr2</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-18</TD><TD ALIGN=RIGHT>38.509%</TD>
  <TD ALIGN=RIGHT>32.607%</TD></TR>
<TR>
  <TH>Rhesus&nbsp;rheMac8</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-14</TD><TD ALIGN=RIGHT>40.165%</TD>
  <TD ALIGN=RIGHT>33.468%</TD></TR>
<TR>
  <TH>Dog&nbsp;canFam3</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-13</TD><TD ALIGN=RIGHT>28.540%</TD>
  <TD ALIGN=RIGHT>30.864%</TD></TR>
<TR>
  <TH>Rabbit&nbsp;oryCun2</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-17</TD><TD ALIGN=RIGHT>24.654%</TD>
  <TD ALIGN=RIGHT>24.981%</TD></TR>
<TR>
  <TH>Cat&nbsp;felCat8</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-17</TD><TD ALIGN=RIGHT>29.520%</TD>
  <TD ALIGN=RIGHT>29.673%</TD></TR>
<TR>
  <TH>Panda&nbsp;ailMel1</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-16</TD><TD ALIGN=RIGHT>30.404%</TD>
  <TD ALIGN=RIGHT>34.777%</TD></TR>
<TR>
  <TH>Cow&nbsp;bosTau8</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-16</TD><TD ALIGN=RIGHT>25.902%</TD>
  <TD ALIGN=RIGHT>25.355%</TD></TR>
<TR>
  <TH>Opossum&nbsp;monDom5</TH>
  <TD>no</TD><TD>254</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-13</TD><TD ALIGN=RIGHT>9.652%</TD>
  <TD ALIGN=RIGHT>7.191%</TD></TR>
<TR>
  <TH>Platypus&nbsp;ornAna2</TH>
  <TD>no</TD><TD>254</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-18</TD><TD ALIGN=RIGHT>6.389%</TD>
  <TD ALIGN=RIGHT>8.652%</TD></TR>
<TR>
  <TH>X. tropicalis&nbsp;xenTro7</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-12</TD><TD ALIGN=RIGHT>4.104%</TD>
  <TD ALIGN=RIGHT>7.913%</TD></TR>
<TR>
  <TH>Chicken&nbsp;galGal5</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2016-05-03</TD><TD ALIGN=RIGHT>3.983%</TD>
  <TD ALIGN=RIGHT>7.853%</TD></TR>
<TR>
  <TH>Turkey&nbsp;melGal5</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-17</TD><TD ALIGN=RIGHT>2.440%</TD>
  <TD ALIGN=RIGHT>4.910%</TD></TR>
<TR>
  <TH>Elephant shark&nbsp;calMil1</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-01-18</TD><TD ALIGN=RIGHT>1.664%</TD>
  <TD ALIGN=RIGHT>4.309%</TD></TR>
<TR>
  <TH>Zebrafish&nbsp;danRer10</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-09-18</TD><TD ALIGN=RIGHT>3.232%</TD>
  <TD ALIGN=RIGHT>5.815%</TD></TR>
</TABLE>